Protein Complex Assembly

This volume details the importance of multiple experimental techniques and computational methods needed to obtain the comprehensive picture of protein complex structure, dynamics and assembly afforded by the emerging field of integrative structural biology. Chapters guide readers through the broad spectrum of approaches required for a complete representation of protein complexes, including expression and purification, experimental characterization of structure and assembly, and computational methods for identifying protein complexes and modelling their assembly. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Protein Complex Assembly: Methods and Protocols aims to ensure successful results in the further study of this vital field.

This volume explores experimental and computational approaches to measuring the most widely studied protein assemblies, including condensed liquid phases, aggregates, and crystals. The chapters in this book are organized into three parts: Part One looks at the techniques used to measure protein-protein interactions and equilibrium protein phases in dilute and concentrated protein solutions; Part Two describes methods to measure kinetics of aggregation and to characterize the assembled state; and Part Three details several different computational approaches that are currently used to help researchers understand protein self-assembly. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Thorough and cutting-edge, Protein Self-Assembly: Methods and Protocols is a valuable resource for researchers who are interested in learning more about this developing field.

This book follows on from Volume 83 in the SCBI series (“Macromolecular Protein Complexes”), and addresses several important topics (such as the Proteasome, Anaphase Promoting Complex, Ribosome and Apoptosome) that were not previously included, together with a number of additional exciting topics in this rapidly expanding field of study. Although the first SCBI Protein Complex book focused on soluble protein complexes, the second (Vol. 87)addressed Membrane Complexes, and the third (Vol. 88) put the spotlight on Viral Protein and Nucleoprotein Complexes, a number of membrane, virus and even fibrillar protein complexes have been be considered for inclusion in the present book. A further book is also under preparation that follows the same pattern, in an attempt to provide a thorough coverage of the subject. Chapter 9 is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

Written by recognized experts in the study of proteins, Proteomics for Biological Discovery begins by discussing the emergence of proteomics from genome sequencing projects and a summary of potential answers to be gained from proteome-level research. The tools of proteomics, from conventional to novel techniques, are then dealt with in terms of underlying concepts, limitations and future directions. An invaluable source of information, this title also provides a thorough overview of the current developments in post-translational modification studies, structural proteomics, biochemical proteomics, microfabrication, applied proteomics, and bioinformatics relevant to proteomics. Presents a comprehensive and coherent review of the major issues faced in terms of technology development, bioinformatics, strategic approaches, and applications Chapters offer a rigorous overview with summary of limitations, emerging approaches, questions, and realistic future industry and basic science applications Discusses higher level integrative aspects, including technical challenges and applications for drug discovery Accessible to the novice while providing experienced investigators essential information Proteomics for Biological Discovery is an essential resource for students, postdoctoral fellows, and researchers across all fields of biomedical research, including biochemistry, protein chemistry, molecular genetics, cell/developmental biology, and bioinformatics.

Given the immense progress achieved in elucidating protein-protein complex structures and in the field of protein interaction modeling, there is great demand for a book that gives interested researchers/students a comprehensive overview of the field. This book does just that. It focuses on what can be learned about protein-protein interactions from the analysis of protein-protein complex structures and interfaces. What are the driving forces for protein-protein association? How can we extract the mechanism of specific recognition from studying protein-protein interfaces? How can this knowledge be used to predict and design protein-protein interactions (interaction regions and complex structures)? What methods are currently employed to design protein-protein interactions, and how can we influence protein-protein interactions by mutagenesis and small-molecule drugs or peptide mimetics?The book consists of about 15 review chapters, written by experts, on the characterization of protein-protein interfaces, structure determination of protein complexes (by NMR and X-ray), theory of protein-protein binding, dynamics of protein interfaces, bioinformatics methods to predict interaction regions, and prediction of protein-protein complex structures (docking and homology modeling of complexes, etc.) and design of protein-protein interactions. It serves as a bridge between studying/analyzing protein-protein complex structures (interfaces), predicting interactions, and influencing/designing interactions.

Photosystem II is a 700-kDa membrane-protein super-complex responsible for the light-driven splitting of water in oxygenic photosynthesis. The photosystem is comprised of two 350-kDa complexes each made of 20 different polypeptides and over 80 co-factors. While there have been major advances in understanding the mature structure of this photosystem many key protein factors involved in the assembly of the complex do not appear in the holoenzyme. The mechanism for assembling this super-complex is a very active area of research with newly discovered assembly factors and subcomplexes requiring characterization. Additionally the ability to split water is inseparable from light-induced photodamage that arises from radicals and reactive O2 species generated by Photosystem II chemistry. Consequently, to sustain water splitting, a “self repair” cycle has evolved whereby damaged protein is removed and replaced so as to extend the working life of the complex. Understanding how the biogenesis and repair processes are coordinated is among several important questions that remain to be answered. Other questions include: how and when are the inorganic cofactors inserted during the assembly and repair processes and how are the subcomplexes protected from photodamage during assembly? Evidence has also been obtained for Photosystem II biogenesis centers in cyanobacteria but do these also exist in plants? Do the molecular mechanisms associated with Photosystem II assembly shed fresh light on the assembly of other major energy-transducing complexes such as Photosystem I or the cytochrome b6/f complex or indeed other respiratory complexes? The contributions to this Frontiers in Plant Science Research Topic are likely to reveal new details applicable to the assembly of a range of membrane-protein complexes, including aspects of self-assembly and solar energy conversion that may be applied to artificial photosynthetic systems. In addition, a deeper understanding of Photosystem II assembly — particularly in response to changing environmental conditions — will provide new knowledge underpinning photosynthetic yields which may contribute to improved food production and long-term food security.

This book illustrates the importance and significance of the molecular (physical and chemical) and evolutionary (gene fusion) principles of protein-protein and domain-domain interactions towards the understanding of cell division, disease mechanism and target definition in drug discovery. It describes the complex issues associated with this phenomenon using cutting edge advancement in Bioinformatics and Bioinformation Discovery. The chapters provide current information pertaining to the types of protein-protein complexes (homodimers, heterodimers, multimer complexes) in context with various specific and sensitive biological functions. The significance of such complex formation in human biology in the light of molecular evolution is also highlighted using several examples. The chapters also describe recent advancements on the molecular principles of protein-protein interaction with reference to evolution towards target identification in drug discovery. Finally, the book also elucidates a comprehensive yet a representative description of a large number of challenges associated with the molecular interaction of proteins.